Combinational test of DGKi with PD-1 blocker

scTCR-seq + scRNA-seq

DGKi

  • DGKs are physiological regulators of T-cell development,differentiation, and function.
  • Inhibition of DGK may restore the T-cell activation program
  • Enhanced effects may be seen with combination therapy (Nivolumab + DGKi)


Data

Sample name: P*****
Condition (1 control, 3 test conditions): CONTROL, CND1, CND2, COMBO
Number of cells : 8096 cells

Initial Processing

## perform default analysis
perform_default_analysis <- function(obj.srt, n_features = 2000, n_pcs = 20, 
                                     dims_for_neighbors = 1:10, 
                                     resolutions = c(0.2, 0.5), 
                                     umap_dims = 1:10) {
  # Step 1: Find variable features
  obj.srt <- FindVariableFeatures(obj.srt, 
                                  selection.method = 'vst', 
                                  nfeatures = n_features)
  
  # Step 2: Scale and normalize data
  all_genes <- rownames(obj.srt)
  obj.srt <- NormalizeData(obj.srt)
  obj.srt <- ScaleData(obj.srt, features = all_genes)
  
  # Step 3: Run PCA
  obj.srt <- RunPCA(obj.srt, 
                    features = VariableFeatures(object = obj.srt), npcs = n_pcs)
  
  # Step 4: Find neighbors
  obj.srt <- FindNeighbors(obj.srt, dims = dims_for_neighbors)
  
  # Step 5: Find clusters
  obj.srt <- FindClusters(obj.srt, resolution = resolutions)
  
  # Step 6: Run UMAP
  obj.srt <- RunUMAP(obj.srt, dims = umap_dims)
  
  # Return the Seurat object with analysis results
  return(obj.srt)
}

# apply
obj.srt <- perform_default_analysis(obj.srt)

Numer of cells

UMAP (sample)

Colored by condition

Colored by each condition

Clustering

UMAP colored by cluster (two resolutions)

Distribution of cells by cluster and condition (res 0.1)

TABLE : Distribution of cells by cluster and condition (res 0.1)

HEATMAP : Distribution of cells by cluster and condition (res 0.1)

Distribution of cells by cluster and condition (res 0.5)

TABLE : Distribution of cells by cluster and condition (res 0.5)

HEATMAP : Distribution of cells by cluster and condition (res 0.5)



# Clonotype Analysis

Clonotype Diversity

CTRL clonotype diversity

CND1 clonotype diversity

CND2 clonotype diversity

COMB clonotype diversity

scRepertoire

Clonotype analysis using scRepertoire

Quantify Clonotypes

Unique clonotypes by TRA chain

Unique clonotypes by TRB chain

Clonotype Abundance

Length of Clonotypes

Compare Clonotypes

Visualize Gene Usage

More Advanced Clonal Analysis

Diversity Analysis


Further Analysis (Specific cell type+clonotype)

Cytotoxic Markers and associated clonotypes

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